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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttatatgcttcttccatgctgtttacaattaatatacctttaaataggattctttttcttccagttttataatattattttatttttctgttcttgttactaaaatgtttttcttgggtgcaaagGTTACCAGTTATTCAAGCGTTGGCTGCAGATGTTAGGCTGACTACCCAATCACTTCTTTCTCAGCTTCTTCAGAAACTTCGCTCAAATATTCAG

Basic information

species Glycine max
transcript GLYMA02G04920.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G04920.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g35290.1 (Oryza sativa), 3'ss of exon 4
gtaagtttatatgcttcttccatgctgtttacaattaatatacctttaaataggattctttttcttccagttttataatattattt-tatttttctgttcttgttactaaaatgtttttcttgggtgcaaagGTTACCAGTTATTCAAGCGTTGGCTGCAGATGTTAGGCTGACTACCCAATCACTTCTTTCTCAGCTTCTTCAGAAACTTCGCTCAAATATTCAG
                                                      | || |||      |  ||||| ||    ||| || ||| |  ||  | | |||    | |   | || | |   ||| ||||| ||||| ||||  || ||||  || || | |  ||| |  || ||| |  ||||||||||||| ||||| ||||| ||||||||||||
---------------------------------------------------gtaagtcatttgacataatctttattatggcctttgtaatttgcaattaatttaactg---tatgccttttcgat-tgaagTTTACCTGTTATCCAAGGCTTAGCTGTTGAAGTCAAGAAGACAATACAGTCATTAATTTCTCAGCTTCTCCAGAAGCTTCGATCAAATATTCAG

upper sequence: GLYMA02G04920.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G006781_T03 (Zea mays), 3'ss of exon 4
gtaagtttatatgcttcttccatgctgtttacaattaatatacctttaaataggattctttttcttccagttttataatattattttatttttctgttcttgttactaaaatgtttttcttgggtgcaaagGTTACCAGTTATTCAAGCGTTGGCTGCAGATGTTAGGCTGACTACCCAATCACTTCTTTCTCAGCTTCTTCAGAAACTTCGCTCAAATATTCAG
                                                    | ||  | | |     | ||  || | | |   | |  |||    |  | |||   |  |  |||| |    |   ||| ||||| ||| | ||||  || ||  | || || | |  |||    |||||| |  |||| |||||||| ||||||||||| ||||||||||||
----------------------------------------------------gtatgttgtgtaacataattgcatcacactccctgacatttgctgttatattaaccatttacttttttccaat-tgaagTTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATCATTAGTTTCACAGCTTCTCCAGAAACTTCGATCAAATATTCAG

upper sequence: GLYMA02G04920.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G11980.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtttatatgcttcttccatgctgtttacaattaatatacctttaaataggattctttttcttccagttttataatattattttatttttctgttcttgttactaaaatgtttttcttgggtgcaaagGTTACCAGTTATTCAAGCGTTGGCTGCAGATGTTAGGCTGACTACCCAATCACTTCTTTCTCAGCTTCTTCAGAAACTTCGCTCAAATATTCAG
                             |    ||  | ||   ||    | ||| ||||| |||   |  | |    |  ||   |   ||  | |||    | ||   | | ||   |   ||  ||| || |||||||| |||||  | || || || ||||| |  || || || |||||||| || |||||||| |||||||| ||||||||||| |||
----------------------------gtgagttttttgtaatctttctcacgatacttttacttaaggcctca----accatc--aagctttagctctaaacatta---tatcttctctctatgtcaagATTGCCAGTTATCCAAGCACTTGCAGCGGAGGTTAGACAAACAACTCAGTCACTTCTCTCACAGCTTCTCCAGAAACTACGCTCAAATATACAG

upper sequence: GLYMA02G04920.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g01350.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtttatatgcttcttccatgctgtttac-aattaatatacctttaaataggattctttttcttccagttttataatattattttatttttctgttcttgttactaaaatgtttttcttgggtgcaaagGTTACCAGTTATTCAAGCGTTGGCTGCAGATGTTAGGCTGACTACCCAATCACTTCTTTCTCAGCTTCTTCAGAAACTTCGCTCAAATATTCAG
|| || || |||  |||||  |||||  || | || ||||||   ||| |   |      |   | |  ||   | |||                    ||   || |    |||||||     |   |||| || ||||| ||||||||  |||||||||| |||||||  || |||||||| ||||||  ||||||||| ||||||||||| |||||||||| |
gtgagcttttat--ttcttgtatgctacttgccaactaatatttgttttagctg------tcaaccttgagaaatgtaa--------------------ctcactattgccctgttttttc---gcttaaagATTGCCAGTCATTCAAGCACTGGCTGCAGAAGTTAGGCAAACAACCCAATCTCTTCTTCATCAGCTTCTCCAGAAACTTCGATCAAATATTCTG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|254335101|gb|GR844886.1|GR844886
EST:     GCCCTAGATTTGGAAGCATTTGTTGGCAAACTTTCAACCATGCATCCAAA                         GTTACCAGTTATTCAAGCGTTGGCTGCAGATGTTAGGCTGACTACCCAATC
genomic: GCCCTAGATTTGGAAGCATTTGTTGGCAAACTTTCAACCATGCATCCAAAgtaagtttat ... gggtgcaaagGTTACCAGTTATTCAAGCGTTGGCTGCAGATGTTAGGCTGACTACCCAATC
EST: gi|254341548|gb|GR852685.1|GR852685
EST:     CAACCATGCATCCAAA                         GTTACCAGTTATTCAAGCGTTGGCTGCAGAAGTTAGGCTGACTACCCAATC
genomic: CAACCATGCATCCAAAgtaagtttat ... gggtgcaaagGTTACCAGTTATTCAAGCGTTGGCTGCAGATGTTAGGCTGACTACCCAATC
EST: gi|193671294|gb|FK613290.1|FK613290
EST:     GCCCTAGATTTGGAAGCATTTGTTGGCAAACTTTCAACCATGCATCCAAA                         GCTACCAGTTATTCAAGCGTTGGCTGCAGATGTTAGGCTGACTACCCAATC
genomic: GCCCTAGATTTGGAAGCATTTGTTGGCAAACTTTCAACCATGCATCCAAAgtaagtttat ... gggtgcaaagGTTACCAGTTATTCAAGCGTTGGCTGCAGATGTTAGGCTGACTACCCAATC
EST: gi|151410266|gb|EV280081.1|EV280081
EST:     AGATTTGGAAGCATTTGTTGGCAAACTTTCAACCATGCATCCAAA                         GTTACCAGTTATTCAAGCGTTGGCTGCAGATGTTAGGCTGACTACCCAATC
genomic: AGATTTGGAAGCATTTGTTGGCAAACTTTCAACCATGCATCCAAAgtaagtttat ... gggtgcaaagGTTACCAGTTATTCAAGCGTTGGCTGCAGATGTTAGGCTGACTACCCAATC
EST: gi|254327754|gb|GR834719.1|GR834719
EST:     GCCCTAGATTTGGAAGCATTTGTTGGCAAACTTTCAACCATGCATCCAAA                         GTTACCAGTTATTCAAGCGTTGGCTGCAGATGTTAG-CTGACTACCCAATC
genomic: GCCCTAGATTTGGAAGCATTTGTTGGCAAACTTTCAACCATGCATCCAAAgtaagtttat ... gggtgcaaagGTTACCAGTTATTCAAGCGTTGGCTGCAGATGTTAGGCTGACTACCCAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatattattttatttttctgttcttgttactaaaatgtttttcttgggtgcaaagGTTACCAGTTATTCAAGCGTTGGCTGCAGATGTTAGGCTGACTACCCAATCACTTCTTTCTCAGCTTCTTCAGAAACTTCGCTCAAATATTCAG
                           tactaaa  putative branch site (score: 1)
                                     tttttcttg  putative PPT
     tattttatttttctgt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttatatgcttcttccatgctgtttacaattaatatacctttaaataggattctttttcttccagttttataatattattttatttttctgttcttgttactaaaatgtttttcttgggtgcaaagGTTACCAGTTATTCAAGCGTTGGCTGCAGATGTTAGGCTGACTACCCAATCACTTCTTTCTCAGCTTCTTCAGAAACTTCGCTCAAATATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT